1. Field of the Invention
The present invention relates to a technique of DNA analysis, and more particularly to a primer design system, a method for designing primers, a storage medium on which is recorded a program for allowing a computer to function as a primer design system, a storage medium on which is recorded data which are necessary during DNA analysis, plates containing primers which are necessary during DNA analysis, a DNA analysis kit comprising a storage medium and primers which are necessary during DNA analysis, and a method for analyzing DNA.
2. Description of the Related Art
In the 1990's, the human genome project has flourished, leading to an increasingly clearer understanding of the genome sequences for E. coli, yeasts, nematodes, rice, Arabidopsis thaliana, mice, rats, humans, and the like. This has been accompanied by a veritable explosion of highly efficient methods for the analysis of nucleotide sequences as well as the development of techniques such as the computerization of sequence analyses and higher throughput in techniques for the analysis of nucleotide sequences of the gene, YAC and BAC libraries, and chromosome markers.
The recent progress of the genome project and the development of sequence analyzing techniques have resulted in the continuing accumulation of massive gene-related databases (see FIG. 1), making bioinformatics increasingly necessary in the data processing of such massive amounts of gene-related data. Bioinformatics is an expression created from biology and informatics (the science of information), meaning research combining life sciences and information sciences, that is, the comprehensive science of handling biological data in its entirety with the intention of making broader use not only of genome data but of biological data, from genes to protein structure or function. At present, however, bioinformatics is not being adequately used in industry-based genetic functional analysis.
Genomic DNA includes both intron and exon regions. Of these, exons encode proteins, making the analysis of exons extremely important in genetic analysis. However, it is extremely difficult to specify exons that are compatible with the actual purpose of research, and conventional genetic analysis has involved selecting exons compatible with the purpose of research merely through trial and error.
FIG. 7 depicts the course of conventional genetic analysis. Conventionally, the individual genes or proteins of interest are generally identified (step 600) by subtraction or DD based cloning of gene, nucleotide sequences or protein amino acid sequences, and then checked what type of functions they have. That is, exons which are considered compatible with the purpose of research are selected beforehand (step 602) from the identified nucleotide sequences to design corresponding primers (step 603). The primers are then used in PCR (polymerase chain reaction) to amplify the target exons (step 604) for analysis of the exons (step 605). PCR is a method in which primers are designed for both ends of the region that is to be amplified, and genes are amplified logarithmically by temperature cycles using a heat resistant DNA enzyme such as Taq DNA polymerase. Primers are oligonucleotides having an —OH at the 3′ end necessary to initiate DNA synthesis.
When the exons selected by the analysis in step 605 prove to be incompatible with the purpose of the research in such conventional genetic analysis, the process (step 606) must be repeated from the exon selection in step 602, making it extremely important to ensure the reliable selection of exons compatible with the purpose of research. During the analysis of differences in gene levels occurring between normal individuals and patients afflicted with a certain disease (such as cancer), for example, exons which are the target of research will be the exons leading to the disease, but it is extremely difficult to determine which exons are the exons in question, and there has been no other way to analyze candidate exons other than by the trial and error described above in order to determine such exons.